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Open Access

Comparison of different computational methods for water structure optimisation

We have compared several computational techniques with the aim to compute the radial distribution function (RDF) as a good characterization of water structure. In particular, we have used molecular mechanic (AMBER99), semi-empirical (AM1, PM3, PM6) and ab initio (DFT) technique. It has been shown that molecular mechanic gives very poor results in the case of water RDF. Ab initio techniques which are in general accepted as very exact methods, in the case of water underestimate intermolecular interaction. Unexpectedly, the semi-empirical method with PM6 parameterisation gives the best results in comparison with RDF measured by X-ray scattering experiment.

Guillot B. A reappraisal of what we have learnt during three decades of computer simulations on water. J Mol Liq. 2002;101:219-260.CrossrefGoogle Scholar

Hao H, Elstner M, Hermans J. Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution. Proteins: Structure, Function and Genetics 2003;50:451-463.Google Scholar